To generate a heatmap you need to select a group of samples you want to compare. Since we’ll be using samples from an existing project, we’ll need to first navigate to that project. Select Public in the right-hand corner of the header bar. This will take you to the list of public projects you can explore.
In the search box in the top left, search for Feline Gingivostomatitis.
Click on the Feline Gingivostomatitis project to navigate to the project folder. You can select a group of samples by checking the box to the left of each sample name. If you want to select all samples in a project, click the checkbox in the upper left corner (1). The number of selected samples will be visible on the top right of the table (2). After selecting at least two samples, click the Heatmap icon (3).
After clicking the Heatmap icon, you should see two options: Taxon Heatmap and AMR Heatmap. These are the two types of heatmaps that you can generate in IDseq. Both let you see summary statistics about groups of samples and can be useful in multi-sample analysis. We are first going to walk through the features of the Taxon Heatmap.
Click on Taxon Heatmap from the dropdown menu. You will then be taken to the heatmap page.
When generating a taxon heatmap, IDseq by default displays the 10 species with the highest reads per million for each sample. You can adjust the number of taxa per sample that are included in the heatmap using the available heatmap filters (see below). Because creating a heatmap pulls in a lot of data, it can sometimes take a few seconds to load when you first create it.
When you first load the heatmap, we preselect a subset of your data so that you are able to experiment with filters and see the results quickly, without having to wait for a full reload each time. These preselect conditions are the following:
- The top 1000 unique taxa per sample, based on relative abundance (rPM)
- Only taxa with at least 5 reads
These conditions define the set of data that is pulled initially when creating the heatmap. Whenever you adjust a filter or view setting, the heatmap will show a subset of this initial set of data.
Add Taxon Button
You can add any taxon that was found in at least one of your samples by using the “Add taxon” button below.